Shinzo Abe, the only head of state in the region who has yet to meet with Kim, made the remarks during an interview with local newspaper Sankei Shimbun.
"I would like to meet Chairman Kim Jong Un of the Korean Workers' Party without condition," Abe said. "I would like to hold a frank conversation."
North Korea has yet to demonstrate a strong interest in a summit with Japan. Pyongyang instead has regularly issued statements condemning Japan for its wartime past, and for its recruitment of Korean comfort women forced to serve in military brothels during World War II.
On Thursday, Abe also complimented Kim, calling him a "leader who can flexibly and strategically evaluate what is best for [his] nation."
Kim has failed to reach a denuclearization deal with the United States, but has continued the summit diplomacy he began in 2018, meeting most recently with Russian President Vladimir Putin in Vladivostok. He has also met Chinese President Xi Jinping more times than with South Korean President Moon Jae-in, who is often credited with easing tensions with the North.
Abe told the Sankei Japan is committed to resolving the issue of Japanese citizens abducted to North Korea and in coordination with the international community.
The statement from the prime minister comes as Japan is using less condemning language in its 2019 diplomatic blue book when addressing North Korea, Kyodo News reported.
Families of abduction victims continue to engage in activism to build awareness in the United States.
Japanese media reported Thursday the families of abductees, including Takuya Yokota, left for Washington to meet with U.S. officials. Yokota was 9 in 1977 when his sister, Megumi, disappeared.
Takuya told reporters he wanted to "express gratitude" to U.S. President Donald Trump for raising the issue of abductions during the U.S.-North Korea summit in Hanoi, Vietnam, and relay the message during meetings with U.S. officials, according to reports.